title: Gene expression changes leading extreme alkaline tolerance in Amur ide (Leuciscus waleckii) inhabiting soda lake.
abstract: BACKGROUND
  Amur ide (Leuciscus waleckii) is an economically and ecologically important cyprinid species in Northern Asia. The Dali Nor population living in the soda lake Dali Nor can adapt the extremely high alkalinity, providing us a valuable material to understand the adaptation mechanism against extreme environmental stress in teleost.
  
  
  RESULTS
  In this study, we generated high-throughput RNA-Seq data from three tissues gill, liver and kidney of L. waleckii living in the soda lake Dali Nor and the fresh water lake Ganggeng Nor, then performed parallel comparisons of three tissues. Our results showed that out of assembled 64,603 transcript contigs, 28,391 contigs had been assigned with a known function, corresponding to 20,371 unique protein accessions. We found 477, 2,761 and 3,376 differentially expressed genes (DEGs) in the gill, kidney, and liver, respectively, of Dali Nor population compared to Ganggeng Nor population with FDR ≤ 0.01 and fold-change ≥ 2. Further analysis revealed that well-known functional categories of genes and signaling pathway, which are associated with stress response and extreme environment adaptation, have been significantly enriched, including the functional categories of "response to stimulus", "transferase activity", "transporter activity" and "oxidoreductase activity", and signaling pathways of "mTOR signaling", "EIF2 signaling", "superpathway of cholesterol biosynthesis". We also identified significantly DEGs encoding important modulators on stress adaptation and tolerance, including carbonic anhydrases, heat shock proteins, superoxide dismutase, glutathione S-transferases, aminopeptidase N, and aminotransferases.
  
  
  CONCLUSIONS
  Overall, this study demonstrated that transcriptome changes in L. waleckii played a role in adaptation to complicated environmental stress in the highly alkalized Dali Nor lake. The results set a foundation for further analyses on alkaline-responsive candidate genes, which help us understand teleost adaptation under extreme environmental stress and ultimately benefit future breeding for alkaline-tolerant fish strains.
authors.affiliation: Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing 100141, China. xupeng@cafs.ac.cn.
authors.forename: Jian
authors.initials: J
authors.lastname: Xu
authors.forename: Qiang
authors.initials: Q
authors.lastname: Li
authors.forename: Liming
authors.initials: L
authors.lastname: Xu
authors.forename: Shaolin
authors.initials: S
authors.lastname: Wang
authors.forename: Yanliang
authors.initials: Y
authors.lastname: Jiang
authors.forename: Zixia
authors.initials: Z
authors.lastname: Zhao
authors.forename: Yan
authors.initials: Y
authors.lastname: Zhang
authors.forename: Jiongtang
authors.initials: J
authors.lastname: Li
authors.forename: Chuanju
authors.initials: C
authors.lastname: Dong
authors.forename: Peng
authors.initials: P
authors.lastname: Xu
authors.forename: Xiaowen
authors.initials: X
authors.lastname: Sun
mesh_terms: D000222:Adaptation, Physiological / Q000187:drug effects / Q000235:genetics*; D000468:Alkalies / Q000494:pharmacology*; D000818:Animals; D003530:Cyprinidae / Q000235:genetics*; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D005880:Gills / Q000187:drug effects / Q000378:metabolism; D007668:Kidney / Q000187:drug effects / Q000378:metabolism; D060106:Lakes; D008099:Liver / Q000187:drug effects / Q000378:metabolism; D058977:Molecular Sequence Annotation; D009928:Organ Specificity / Q000187:drug effects / Q000235:genetics; D012015:Reference Standards; D015203:Reproducibility of Results; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012641:Selection, Genetic; D017423:Sequence Analysis, RNA; D059467:Transcriptome / Q000235:genetics
chemical_list: D000468:Alkalies